quarta-feira, janeiro 30, 2013

Received 01 July 2012 Accepted 04 October 2012 Published online 09 December 2012

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Abstract

Recent evidence suggests that a variety of organisms may harness some of the unique features of quantum mechanics to gain a biological advantage. These features go beyond trivial quantum effects and may include harnessing quantum coherence on physiologically important timescales. In this brief review we summarize the latest results for non-trivial quantum effects in photosynthetic light harvesting, avian magnetoreception and several other candidates for functional quantum biology. We present both the evidence for and arguments against there being a functional role for quantum coherence in these systems.

Identifying terrestrial planets in the habitable zones (HZs) of other stars is one of the primary goals of ongoing radial velocity and transit exoplanet surveys and proposed future space missions. Most current estimates of the boundaries of the HZ are based on 1-D, cloud-free, climate model calculations by Kasting et al.(1993). The inner edge of the HZ in Kasting et al.(1993) model was determined by loss of water, and the outer edge was determined by the maximum greenhouse provided by a CO2 atmosphere. A conservative estimate for the width of the HZ from this model in our Solar system is 0.95-1.67 AU.

Here, an updated 1-D radiative-convective, cloud-free climate model is used to obtain new estimates for HZ widths around F, G, K and M stars. New H2O and CO2 absorption coefficients, derived from the HITRAN 2008 and HITEMP 2010 line-by-line databases, are important improvements to the climate model. According to the new model, the water loss (inner HZ) and maximum greenhouse (outer HZ) limits for our Solar System are at 0.99 AU and 1.70 AU, respectively, suggesting that the present Earth lies near the inner edge. Additional calculations are performed for stars with effective temperatures between 2600 K and 7200 K, and the results are presented in parametric form, making them easy to apply to actual stars. The new model indicates that, near the inner edge of the HZ, there is no clear distinction between runaway greenhouse and water loss limits for stars with T_{eff} ~< 5000 K which has implications for ongoing planet searches around K and M stars. To assess the potential habitability of extrasolar terrestrial planets, we propose using stellar flux incident on a planet rather than equilibrium temperature. Our model does not include the radiative effects of clouds; thus, the actual HZ boundaries may extend further in both directions than the estimates just given.

Comments: Accepted to Astrophysical Journal. 39 pages, 9 figures. An online habitable zone calculator (and a FORTRAN code) is available at (this http URL) or at first author's website

NOT having any family is tough. Often unappreciated and uncomfortably different, orphans have to fight to fit in and battle against the odds to realise their potential. Those who succeed, from Aristotle to Steve Jobs, sometimes change the world.

Who would have thought that our DNA plays host to a similar cast of foundlings? When biologists began sequencing genomes, they discovered that up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers, and a few even seem have played a part in the evolution of the human brain.

But where do they come from? With no obvious ancestry, it was as if these genes had appeared from nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t …

(This article belongs to the Special Issue Biosemiotic Entropy: Disorder, Disease, and Mortality)

Abstract:

Biosemiotic entropy involves the deterioration of biological sign systems. The genome is a coded sign system that is connected to phenotypic outputs through the interpretive functions of the tRNA/ribosome machinery.This symbolic sign system (semiosis) at the core of all biology has been termed “biosemiosis”. Layers of biosemiosis and cellular information management are analogous in varying degrees to the semiotics of computer programming, spoken, and written human languages.Biosemiotic entropy — an error or deviation from a healthy state — results from errors in copying functional information (mutations) and errors in the appropriate context or quantity of gene expression (epigenetic imbalance). The concept of biosemiotic entropy is a deeply imbedded assumption in the study of cancer biology. Cells have a homeostatic, preprogrammed, ideal or healthy state that is rooted in genomics, strictly orchestrated by epigenetic regulation, and maintained by DNA repair mechanisms. Cancer is an eminent illustration of biosemiotic entropy, in which the corrosion of genetic information via substitutions, deletions, insertions, fusions, and aberrant regulation results in malignant phenotypes. However, little attention has been given to explicitly outlining the paradigm of biosemiotic entropy in the context of cancer. Herein we distill semiotic theory (from the familiar and well understood spheres of human language and computer code) to draw analogies useful for understanding the operation of biological semiosis at the genetic level. We propose that the myriad checkpoints, error correcting mechanisms, and immunities are all systems whose primary role is to defend against the constant pressure of biosemiotic entropy, which malignancy must shut down in order to achieve advanced stages. In lieu of the narrower tumor suppressor/oncogene model, characterization of oncogenesis into the biosemiotic framework of sign, index, or object entropy may allow for more effective explanatory hypotheses for cancer diagnosis, with consequence in improving profiling and bettering therapeutic outcomes.

"I think we need to move away from treating a strict RNA world scenario as the central accepted answer for the origin of life because most of the origin of life community don't think that's the definitive answer." -- Sara Imari Walker

Is next week's Origins of Life conference at Princeton University the RNA world's last hurrah? The Origin of Life community has largely rejected the RNA world, biochemist Pier Luigi Luisi recently describing it to me as a baseless fantasy. I asked physicist Sara Walker to weigh in. Walker is on the adjunct faculty at Arizona State University, a NASA postdoc fellow who is one of the presenters at the upcoming Princeton conference.

Long embraced by NASA despite decades of failed experiments, the RNA world is the organizing point for the Princeton gathering, which is co-sponsored by NASA. Walker acknowledges that the Origin of Life community does not think the RNA world is "the definitive answer." And NASA's award of $8 million in September of last year to Carl Woeseet al. is proof that origin of life remains a largely philosophical discussion, with Woese telling me in October (sadly he died in December) that we don't know what life is, and that his grant to study the principles of the origin and evolution of life signalled that NASA is rethinking its approach to the origin of life problem.

Walker, who is a collaborator of ASU's Beyond Center director, Paul Davies, says she also finds inspiration in the work of Carl Woese and Nigel Goldenfeld regarding collective evolution and horizontal gene transfer along with the ideas of Stuart Kauffman and others on self-organization as an evolutionary process.

Walker thinks "biological systems are dictated by the flow of information . . . how information is handled and processed can distinguish living from nonliving."

One of the interesting points of the Princeton conference is the attempt to open it up to parties beyond presenting scientists. A good thing. What's the big secret anyway? That the RNA world is a bust? That public money has been wasted?

The conference should be wide open to the public, held in a theater like the World Science Festival is, and streamed over the Internet. Public funding might then be a lot easier to come by for Origin of Life researchers.

Here's an internal email from the principal organizer of the Princeton conference, Laura Landweber, which I was able to access, discussing the possibilities of informing a wider audience.

"From: Laura Landweber lfl@princeton.edu

Date: December 29, 2012 9:35:25 AM EST

To: Recipient List Suppressed

Subject: remember to register for Origin of Life conference

If you plan on attending many of the origin of life talks the week of Jan. 21-24, then please register (which is free), because the room capacity is almost full, and then the meeting will be closed to registration (but we are working on webcasts, and there's also a video monitor outside the lecture room)".

Excerpts of my interview with Sara Walker follow.

Sara Walker has a BS in Physics from Florida Institute of Technology and a PhD in Physics and Astronomy from Dartmouth College. Prior to ASU, she was a postdoctoral fellow at NSF/NASA Center for Chemical Evolution at the Georgia Institute of Technology.

Suzan Mazur: It's good to see that about a third of the presenters are women at the Princeton Origins of Life conference next week, where you are a featured speaker as well.

Sara Walker: Yes.

Suzan Mazur: You were co-organizer of the Women Science Mentoring Program at Dartmouth a couple of years ago, which paired graduate women scientists with high school girls. Would you talk a little about the success of that mentoring program?

Sara Walker: It was indeed very successful. We took a group mentoring approach. A few graduate women in science met weekly with high school girls who had demonstrated a strong interest in science. It was so much fun. These girls lit up when we talked about dissecting frogs and things like that. It was not the kind of conversation they were used to having.

They also didn't really know what the college experience was like. We had an opportunity to walk them through it and introduce them to new ideas. It inspired me to see them inspired, so excited, wanting to know how to get into science while still in high school. Because when I was their age I wasn't sure what the world of science was all about.

Suzan Mazur: You're now collaborating with the esteemed Paul Davies, director of the Beyond Center at Arizona State University. Can you tell me when you first became interested in science?

Sara Walker: My interest in science began in high school but I didn't know what specifically I wanted to do in science. It was at Cape Cod Community College in Massachusetts, which I attended for two years, where I decided that I wanted to actually be a scientist. I took a physics class first term with Professor Shaw. I can still remember walking in to Prof. Shaw's class the first day and Prof. Shaw telling us about magnetic monopoles, these very illusive objects that had been predicted by theory but had never been identified in the laboratory. It was mindboggling to me. I was so excited about being enabled to then go out and look for these things.

After CCCC, I really wanted to be a physicist. I thought scientists who did theoretical physics, particle physics and cosmology were the absolute coolest people on the planet. I continued my undergraduate work at Florida Institute of Technology and then went to Dartmouth where I worked with Marcelo Gleiser.

Suzan Mazur: Marcelo Gleiser was your PhD advisor at Dartmouth, the Brazilian scientist, who is one of the participants at the upcoming Origin of Life meeting at CERN.

Sara Walker: Marcelo really got me interested in astrobiology and the origin of life. He told me that cosmology was cool but that he'd just started a project on origin of life and would I be interested in participating. I said sure.

Suzan Mazur: You've written a paper recently with Paul Davies called "The Algorithmic Origins of Life." Would you establish what you mean by an algorithm?

Sara Walker: An algorithm, in the context of the paper, is a program that allows the active use of information -- information processing -- which is really important to biological systems. It's not just that biological systems store their information in molecules like DNA, but that they actively use this information to operate.

Suzan Mazur: So the algorithm is a program that allows the active use of information. What about the information itself?

Sara Walker: Information can be loosely defined as events that affect and direct the state of a dynamic system. Saying that information is algorithmic really means that specific events are programmed to have specific outcomes in biological systems. So it's really the processing of the information that's unique about how biology operates.

Suzan Mazur: You say that at some point "information gains direct, and context-dependent causal efficacy over the matter it is instantiated in". What is the information you refer to?

Sara Walker: In this case it is the state of the system, an example the connections or topology of a biochemical network, so it is highly distributed. Function arises due to the distribution of information, therefore biologically meaningful information only arises in the context of the wider system.

Suzan Mazur: In your paper you discuss progress being made in understanding where and when origin of life happened. Other scientists I've interviewed differ. Gunter von Kiedrowski, for example, has told me the following: "We can't travel back in time, we'll never know the historical course [of the origin of life]." Steen Rasmussen told me essentially the same.

And Doron Lancet said this: "We will likely never know what were actually the exact chemical substances that began life. But we can wisely guess what principles such chemicals had to obey."

Would you comment?

Sara Walker: I do agree with those statements. The point is we've made a lot of progress looking at isolated parts of the problem. Identifying what some of the conditions on early Earth were and what you can synthesize under those conditions, what in biology seems to be essential molecules. But to move beyond that and prove an origins story, that's where you really need to get the deeper principles. The examples you gave from von Kiedrowski, Rasmussen and Lancet point to the fact that while we may never know the precise details of the chemistry or the exact sequence of events, we may still figure out the deeper principles at work.

Suzan Mazur: Doron Lancet also told me that we can't even say there were lipids way back when, that what existed might have been lipid-like. And he said it's also very assuming for us to be thinking that the way life is now with 20 amino acids and four nucleotides is "how life should have been from its inception" -- it could have been any set of molecules jump-starting life.

Sara Walker: I totally agree with that.

Suzan Mazur: So have we made progress on when and where it happened if we don't know what the chemicals were and it doesn't matter what the exact circumstances were? Lancet said further: " [I]f people tell you life began at a temperature of 25 degrees Centigrade, 110 degrees or 360 degrees (in suboceanic vents) -- this doesn't matter. What does matter, is the principle of what would constitute acceptable molecular roots of life, and at the same time have sufficient simplicity to warrant emergence from an abiotic mixture of chemicals."

Sara Walker: We don't even know which chemical systems came first. There's a huge debate between lipids or genetic polymers or peptides. We just don't know, and I agree the best way to find answers is to look at more general principles than precise chemical details.

Suzan Mazur: So all three questions are still up in the air -- when, where and how.

Sara Walker: Yes. We definitely are still up in the air in the origins of life investigation. But one of the reasons I'm optimistic about making headway in uncovering the deeper conceptual principles about origins of life -- the how -- is that scientists are understanding biology better. We're looking at things at a mechanistic level, observing biological systems operate, i.e., how protein networks function, etc. The problem is that we have to extrapolate from the chemistry and specific details of the life we know to try to figure out the more universal ideas that might be characteristic of any living system including those we haven't identified yet. That's really the hard part.

Suzan Mazur: Do you agree with the late Carl Woese that our Last Universal Common Ancestor was a process not something material?

Sara Walker: Yes. I'm a very big fan of Carl Woese's work. He's had a lot of brilliant insights into early evolution.

Suzan Mazur: It's very sad that he's gone, he had so much more to say.

The last few decades have witnessed the burgeoning of many highly productive lines of investigation into abiogenesis and the early emergence of biological complexity. Planetary sciences and geochemistry have produced a short-list of well-studied settings where prebiotic chemistry may have led to the transition from non-living to living matter. Major advances in abiotic syntheses of important biomolecules have resulted in an improved understanding of the relative availabilities of proto-biomolecules. The continuing growth of bioinformatics databases has given computational biologists an unprecedented ability to reconstruct the properties of early organisms and ancient evolutionary histories. Synthetic biology now allows investigators to examine the boundaries of life's genetic systems and minimal life in the laboratory. In general, the advance of astrobiology has expanded our understanding of habitability and life as cosmological phenomena. This workshop will integrate these themes, foster new local, national and international collaborations, and actively encourage scientists from within and outside the Princeton community to pursue studies of life's origins. The workshop program will bring together researchers in these disparate subjects and subfields to address the questions of life's origins in the astronomical, chemical, genetic, evolutionary, and information-theoretic contexts.

"I think we need to move away from treating a strict RNA world scenario as the central accepted answer for the origin of life because most of the origin of life community don't think that's the definitive answer." - Sara Imari Walker

Received 07 January 2012 Accepted 24 October 2012 Published online 19 December 2012

Abstract

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

Abstract

Gene duplications are believed to facilitate evolutionary innovation.However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

Author Summary

Darwin's theory of evolution is one of gradual change, yet evolution sometimes takes remarkable leaps.Such evolutionary innovations are often linked to gene duplication through one of three basic scenarios: an extra copy can increase protein levels, different ancestral subfunctions can be split over the copies and evolve distinct regulation, or one of the duplicates can develop a novel function.Although there are numerous examples for all these trajectories, the underlying molecular mechanisms remain obscure, mostly because the preduplication genes and proteins no longer exist. Here, we study a family of fungal metabolic enzymes that hydrolyze disaccharides, and that all originated from the same ancestral gene through repeated duplications. By resurrecting the ancient genes and proteins using high-confidence predictions from many fungal genome sequences available, we show that the very first preduplication enzyme was promiscuous, preferring maltose-like substrates but also showing trace activity towards isomaltose-like sugars. After duplication, specific mutations near the active site of one copy optimized the minor activity at the expense of the major ancestral activity, while the other copy further specialized in maltose and lost the minor activity. Together, our results reveal how the three basic trajectories for gene duplicates cannot be separated easily, but instead intertwine into a complex evolutionary path that leads to innovation.

Funding: S. Maere and K. Vanneste are fellows of the Fund for Scientific Research-Flanders (FWO). Research in the lab of KJV is supported by the Human Frontier Science Program, ERC Starting Grant 241426, VIB, EMBO YIP program, KU Leuven, FWO, IWT and the AB InBev Baillet-Latour foundation. Research in the lab of SM is supported by VIB, Ghent University, FWO and IWT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

↵*Corresponding author: E-mail: koonin@ncbi.nlm.nih.gov

Received October 3, 2012.

Revision received December 7, 2012.

Accepted January 4, 2013.

Abstract

Evolution of prokaryotes involves extensive loss and gain of genes which lead to substantial differences in the gene repertoires even among closely related organisms. Through a wide range of phylogenetic depths, gene frequency distributions in prokaryotic pangenomes bear a characteristic, asymmetrical U-shape, with a core of (nearly) universal genes, a “shell” of moderately common genes, and a “cloud” of rare genes. We employ mathematical modeling to investigate evolutionary processes that might underlie this universal pattern. Gene frequency distributions for almost 400 groups of 10 bacterial or archaeal species over a broad range of evolutionary distances were fit to steady state, infinite allele models based on the distribution of gene replacement rates and the phylogenetic tree relating the species in each group. The fits of the theoretical frequency distributions to the empirical ones yield model parameters and estimates of the goodness of fit. Using the Akaike Information Criterion, we show that the neutral model of genome evolution, with the same replacement rate for all genes, can be confidently rejected. Of the three tested models with purifying selection, the one in which the distribution of replacement rates is derived from a stochastic population model with additive per-gene fitness yields the best fits to the data. The selection strength estimated from the fits declines with evolutionary divergence while staying well outside the neutral regime. These findings indicate that, unlike some other universal distributions of genomic variables, e.g. the distribution of paralogous gene family membership, the gene frequency distribution is substantially affected by selection.

quinta-feira, janeiro 17, 2013

"Of 6,193 papers we surveyed in more than 100 peer-reviewed journals, only 17% present accessible trees and alignments (used to infer relatedness). Contacting lead authors to procure data sets was only 19% successful. DNA sequences were deposited in GenBank for almost all these studies, but it is the actual character alignments that are pivotal for reproducing phylogenetic analyses. We estimate that more than 64% of existing alignments or trees are permanently lost. (Emphasis added.)

This problem will increasingly hinder phylogenetic inference as the use of whole-genome data sets becomes common. Journals need to reinforce a policy of online data deposition, either as supplementary material or in repositories such as TreeBASE (http://treebase.org) or Dryad (http://datadryad.org) -- including for data sets based on previously published sequences. Ecologists, evolutionary biologists and others will then have access to rigorous phylogenetics for testing their hypotheses.

At least that is what some scientists in the phylogenetic community argue, because only about four percent of all published phylogenies are stored in places such as TreeBASE or Dryad. Their message is quite simple: it is time to bring together more databases with estimations on how species are possibly related to each other.

Several journals in the evolutionary biology field recently adopted policies that encourage or require contributors to make their data publicly available online. Yet, this only leads to the storage of a very small percentage of ten-thousands of phylogenies that have been constructed in the past few decades.

Sometimes you wonder whether the glass is half full or half empty. But when it is only filled for four percent -- the other 96 percent is just air -- there is only one conclusion: it is time for more.
Queria ver a cara de alguns mandarins da Nomenklatura científica e da Galera dos meninos e meninas de Darwin... A Árvore da Vida é uma ilusão... projeção de mentes mesmerizadas pelo materialismo filosófico que não se rendem às evidências encontradas na natureza...

Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification.

Chemical evolution includes the capture, mutation, and propagation of molecular information and can be manifested as coordinated chemical networks that adapt to environmental change. The robustness of a chemical network depends on the diversity of its membership, which establishes the probability for the successful selection of superior chemical species and populations. A dynamic exchange of network component structures and assemblies, via both covalent and noncovalent associations, is fundamental for the network’s ability to learn, to capture and integrate information about an environment that ensures the network’s future response to similar conditions, as an inherent part of chemical evolution.In considering the origins of chemical evolution or discovering the simplest molecular systems capable of promulgating intelligent behavior, we acknowledge that merely defining the terms learning, intelligence, and evolution at a molecular level remains a significant part of our challenge in this Accounts of Chemical Research issue.The origins of life on Earth, the remarkable result of chemical evolution through emerging self-assembly into ever-increasing hierarchical complexity in structure and function, remains one of the greatest research challenges of our time. Our understanding of reaction dynamics and energetics, growing insight in dynamic combinatorial systems, increasing refinement of models for the structures of supramolecular assemblies, and expanding knowledge of the cooperative interactions of biopolymers in present-day cells suggest that the timing of this special issue could not be more appropriate. We therefore begin our discussion with the small molecules, including sugars, nucleosides, lipids, and amino acids, that were likely members of a diverse and rich prebiotic inventory and the clear role the emergence of chirality of these building blocks plays in the selection and amplification processes from which modern biochemistry appeared. The discussion extends to the general concept of molecular complementarity, which underpins the development of all supramolecular assemblies, and certainly those containing hydrogen-bonded or metal-coordinated complexes capable of self-replication through dynamic response to fluctuating environmental stimuli.The Darwinian threshold required for appearance of the biological cell underscores the development of “self” versus “non-self” in these chemical networks. The barriers that define dynamic chemical systems as uniquely self must be physically and kinetically selective to permeability, primarily of nutrient molecules that maintain network viability. The approaches presented in this issue evaluate roles of atmospheric flux, lipid-like compartmentalization, and self-replicating protocells in creating nanoscale assemblies that could provide the necessary features of a cellular system. As the components of cellular structure accrete, the ability to transduce energy from the environment in order to maintain dynamic functions removed from thermodynamic equilibrium is a critical step along the path to complex cellular life. Experimental systems that execute photochemically driven redox cycling and that generate chemical gradients to impel systems toward synthetic complexity and ordered structure are also described. The role of noncovalent interactions and new approaches to creating dynamic covalent assemblies is further explored in the emergence of both digital and analog information arising from molecular assemblies.These diverse approaches to deconvolution and reintegration of the origins of the cell, projected in collaboration through the lens of chemical evolution, suggest a remarkable degree of intrinsic molecular intelligence that guide the bottom-up emergence of living matter. However, this idea of molecular intelligence is certainly not new. Charles Darwin imagined a chemically rich “warm pond” from which evolution originated, and his idea was published almost 100 years before the duplex structure of DNA was proposed. A population of simple molecules, storing and copying information to ensure their own survival prebiotically, argues that intelligent behavior is not restricted to complex genomes but is an inherent property of matter. Darwin’s hypothesis further predicts the emergence of new intelligent materials, ones not limited to what can be deduced from biology’s “archeological” remnants but even more diverse and exotic realms of dynamic chemical systems that might never have been explored by extant biochemistry.While our objective is to decipher the evolutionary rules that directed the transition from inanimate matter to life, we recognize that the march of molecular history likely had many pathways. Accordingly, this issue circumscribes the functional concepts, leveraging Nature’s platforms for molecular information, using its existing chemical inventory or libraries, and, with selective and judicious tinkering along the way, elaborates the basic rules of bottom-up self-assembly guided by both digital and analog molecular recognition systems. In addition, the diversity in approaches to understanding and employing chemical evolution is as important as the diversity in chemical composition required to promulgate evolution itself and suggests that collaboration among these diverse approaches to gaining insights into chemical evolution and working toward the interfaces among them will be extraordinarily rich with opportunities. Although not an exhaustive survey, we hope that this special issue will inspire the broader scientific community to elaborate and expand efforts in this research realm and to seek synchronicity with systems biology as the top-down complementary approach to deciphering the origins and function of living matter, to look forward to how we can design and construct new intelligent materials that address the grand challenges we face as a society, and to look outward, to other worlds that may harbor life in ways that such insights into chemical evolution may help us better understand, anticipate, and recognize.